Clinical Bioinformatician - Clinical Genomics Laboratory

Regeneron Clinical Genomics Laboratory LLC; United States; Hybrid; USD 96,000 - 156,000; Full time

Benefits offered by this job

Annual bonuses

Equity awards

Health benefits

Paid time off

Job summary

Regeneron Pharmaceuticals, Inc. in Tarrytown, NY is seeking an experienced Clinical Bioinformatician to lead optimization, validation, and production support of NGS-based bioinformatics pipelines in a regulated CLIA setting.

The role requires strong independence and collaboration across scientific, operational, and leadership teams. The candidate will oversee analytical validation, production pipeline operations, tool evaluation, change management, and data governance.

Qualifications

• Masters or equivalent in bioinformatics or computational biology; CLIA-regulated clinical genomics exposure is a plus.
• Hands-on experience validating NGS workflows in a CLIA environment; knowledge of AMP/CAP guidelines.
• Experience with short-read sequencing data, QC, demultiplexing, and troubleshooting.

Responsibilities

• Lead validation, revalidation, and optimization of clinical NGS pipelines; define QC thresholds.
• Oversee daily production of validated pipelines; monitor runs and samples; troubleshoot issues.
• Evaluate and select bioinformatics tools; inform build-vs-buy decisions.
• Support change management, version control, and regulatory documentation.
• Contribute to pipeline development, containerization, and workflow orchestration.
• Manage data governance and regulatory compliance; ensure audit-ready records.
• Monitor cloud compute/storage costs and report to leadership.

Skills

NGS validation

Pipeline optimization

CLIA experience

Python

R

Linux/Unix

Data governance

Communication

Education

Master's degree in Bioinformatics

Bachelor's with CLIA experience

Tools

GATK

BWA

SAMtools

VCF tools

Job description

Build Our Future Together

We are seeking an experienced Clinical Bioinformatician to join the Regeneron Clinical Genomics Laboratory and lead the optimization, validation, and production support of NGS-based bioinformatics pipelines in a regulated clinical diagnostic environment. The ideal candidate will bring a proven track record in a CLIA-regulated laboratory, the ability to work independently, and strong communication skills to collaborate across scientific, operational, and leadership teams.

When & where: Work Location: Tarrytown, NY Hybrid: 4 days per week on site

Discover your role

• NGS pipeline validation & optimization: Lead or co-lead analytical validation and revalidation of NGS bioinformatics pipelines for clinical assays, including germline and future disease applications. Optimize sensitivity, specificity, limit of detection, and variant allele fraction thresholds using clinical samples and in silico data sets. Define and document pipeline configurations, filtering criteria, and QC thresholds in accordance with AMP/CAP best practice guidelines and applicable CLIA, CAP, and state regulatory requirements.
• Bioinformatics tool evaluation & selection: Benchmark and select tools for alignment, variant calling, annotation, and quality control based on assay design, specimen type, and sequencing platform. Inform build-versus-buy decisions through technical evaluation of vendor-supplied pipeline solutions.
• Production pipeline operations: Oversee daily execution of validated clinical pipelines and monitor performance across sequencing runs and patient samples through QC programs and key performance indicators. Troubleshoot pipeline failures, data quality issues, and software errors;escalate complex problems to the Laboratory Director as appropriate.
• Change management & version control: Support pipeline updates through impact assessment, revalidation planning, and change documentation. Apply version control best practices throughout development and release to maintain traceability and regulatory compliance.
• Pipeline development support: Contribute to the design and development of new or updated pipelines, incorporating selected tools, containerization, and workflow orchestration.
• Data management & regulatory compliance: Manage genomic and patient data in accordance with applicable privacy laws and federal, state, and institutional data security policies. Maintain audit-ready records of pipelines, validation studies, software versions, and standard operating procedures. Support data integrity through verification, sample identifier management, and audit logging.
• Cost monitoring & resource management: Track and report cloud compute and storage usage, software license costs, and vendor tool expenditures. Flag cost trends and anomalies, identify savings opportunities that preserve clinical performance and compliance, and provide usage data and trend summaries to support leadership’s budget planning.

This role requires

• Master's degree in Bioinformatics, Computational Biology, Genomics, or a related field.
• A Bachelor's degree with substantial hands‑on experience in a CLIA-regulated clinical genomics or molecular diagnostics laboratory is accepted in lieu of a Master's degree.
• 2–4 years of experience in a clinical molecular diagnostics or clinical genomics laboratory, with demonstrated hands‑on NGS bioinformatics pipeline validation experience in a CLIA-regulated setting.
• Proven experience performing or supporting NGS bioinformatics pipeline validation in a CLIA-regulated clinical laboratory, including establishing sensitivity, specificity, limit of detection, and VAF thresholds.
• Experience with short‑read sequencing data from high‑throughput platforms, including run‑level and sample‑level QC, demultiplexing, and troubleshooting data quality issues.
• Hands‑on experience validating, configuring, and supporting commercial or vendor‑supplied secondary analysis and variant interpretation platforms in a clinical setting, including managing software updates, settings, and filtering criteria.
• Working knowledge of NGS file formats (FASTQ, BAM/CRAM, VCF) and standard tools for alignment, variant calling, annotation, and quality control, with the ability to benchmark vendor and open‑source tools against one another.
• Proficiency in Linux/Unix environments and in Python or R, including scripting for QC, data analysis, and integration or automation around vendor platforms.

Does this sound like you?

We are committed to building a workplace with an inclusive culture. Regeneron is an equal‑opportunity employer and all qualified applicants will receive consideration for employment without regard to race, color, religion or belief (or lack thereof), sex, sexual orientation, gender identity or expression, gender reassignment, marital or civil partnership status, civil status, pregnancy or parental status, age, disability, nationality, citizenship status, ethnic or national origin, membership of the Traveler community, familial status, genetic information, military or veteran status, or any other characteristic protected under applicable law. Where required, we will provide reasonable accommodation to applicants with known disabilities or chronic illnesses during the recruitment process, unless such accommodation would impose undue hardship. Where necessary, we disclose salary ranges for roles in all countries in which we operate. The final offer will be determined within the relevant range based on the country of employment, specific role level, and your skills and experience. In some countries, collective bargaining agreements (CBAs) may apply and influence certain elements of pay or benefits. Regeneron offers a competitive and comprehensive total rewards package which may include, depending on country and role:

• annual bonuses or other incentive plans
• equity awards
• pension or retirement benefits
• 401(k) company match
• health and wellness programs
• fitness centers
• insurance benefits (e.g. medical, dental, vision, life and disability)
• paid time off
• family support benefits

For additional information about Regeneron benefits in the U.S., please visit https://careers.regeneron.com/en/working-at-regeneron/total-rewards/. For other locations, additional information will be provided during the recruitment process. Please be advised that at Regeneron, we believe we do our best work when we are together. For that reason, many roles are required to be performed on‑site. As part of the recruitment process, certain background checks may be conducted in accordance with the laws of the country where the position is based. The purpose of such checks is to verify certain information prior to the commencement of employment such as identity, right to work and educational qualifications. For jobs in Canada: this posting is for an existing position. Salary Range (annually) $95,800.00 - $156,400.00 Regeneron is a leading biotechnology company that invents life-transforming medicines for people with serious diseases. Founded and led for over 30 years by physician-scientists, our unique ability to repeatedly and consistently translate science into medicine has led to nine FDA-approved treatments and numerous product candidates in development, almost all of which were homegrown in our laboratories. Our medicines and pipeline are designed to help patients with eye diseases, allergic and inflammatory diseases, cancer, cardiovascular and metabolic diseases, neurology, infectious diseases and rare diseases. Regeneron is also proud of award winning culture of innovation, being recognized as a Great Place to Work in 2021, Fast Company’s Best Workplace for Innovators in 2020, and Forbes JUST companies in 2020, among others.